Locus 1297

Sequence ID 3R_DroMel_CAF1
Location 3,820,074 – 3,820,227
Length 153
Max. P 0.999313
window2116 window2117 window2118

overview

Window 6

Location 3,820,074 – 3,820,194
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.50
Mean single sequence MFE -38.54
Consensus MFE -30.87
Energy contribution -32.95
Covariance contribution 2.08
Combinations/Pair 1.03
Mean z-score -2.36
Structure conservation index 0.80
SVM decision value 1.88
SVM RNA-class probability 0.981257
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3820074 120 + 27905053
AGUAGCGGCGGCGAUUGGUUAACCCACUGGGGUUUUUUCUCUCGAAUUUGCAGAGCUGCUGAAUGAAUAUGAAAAUCACUGGAUUUCUACACAGCAGCAGCAUCUGCAAUGAUGGGCCGA
.....((((..(((..((..(((((....)))))...))..)))...((((((((((((((.........((((.((....)))))).......))))))).)))))))......)))). ( -41.69)
>DroSec_CAF1 47847 116 + 1
AGCGGCG---GCGAUUGGUUAACCCACUGGGGUUUUUUCUCUCGAAUUUGCAGAGCUGCUGAAUGAAUAUGAAAAUCACUGGAUUUCUACAC-CCAGCAGCAUCUGCAAUGAUGGGCCGA
..((((.---.(((..((..(((((....)))))...))..)))...((((((((((((((..((.....((((.((....))))))..)).-.))))))).)))))))......)))). ( -41.40)
>DroSim_CAF1 52434 119 + 1
AGCGGCGGUGGCGAUUGGUUAACCCACUGGGGUUUUUUCUCUCGAAUUUGCAGAGCUGCUGAAUGAAUAUGAAAAUCACUGGAUUUCUACAC-CCAGCAGCAUCUGCAAUGAUGGGCCGA
..((((.....(((..((..(((((....)))))...))..)))...((((((((((((((..((.....((((.((....))))))..)).-.))))))).)))))))......)))). ( -41.40)
>DroEre_CAF1 39260 105 + 1
-----------CGAUUGGUUAACCCACUGGGGUUUUUUCUCUCGAAUUUGCAGAGC---UGAAUGAAUAUGAAAAUCACUGGAUUUCUACAC-CCAGCAGCAUCUGCAAUGAUGGGCCAA
-----------...(((((((((((....))))).............(((((((((---((........((.....))((((..........-)))))))).))))))).....)))))) ( -28.60)
>DroYak_CAF1 51654 116 + 1
CGCGGCAGCGUCGAUUGGUUAACCCACUGGGGUUUUUUCUCUCGAAUUUGCAGAGC---UGAAUGAAUAUGAAAAUCACUGGAUUUCUACAC-CCAGCAGCAUCUGCAAUGAUGUGCCGA
..(((((.((((((..((..(((((....)))))...))..))....(((((((((---((........((.....))((((..........-)))))))).))))))).))))))))). ( -39.60)
>consensus
AGCGGCGG_GGCGAUUGGUUAACCCACUGGGGUUUUUUCUCUCGAAUUUGCAGAGCUGCUGAAUGAAUAUGAAAAUCACUGGAUUUCUACAC_CCAGCAGCAUCUGCAAUGAUGGGCCGA
..((((.....(((..((..(((((....)))))...))..)))...((((((((((((((.........((((.((....)))))).......))))))).)))))))......)))). (-30.87 = -32.95 +   2.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 3,820,074 – 3,820,194
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.50
Mean single sequence MFE -41.52
Consensus MFE -33.84
Energy contribution -35.44
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -4.01
Structure conservation index 0.82
SVM decision value 3.50
SVM RNA-class probability 0.999313
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3820074 120 - 27905053
UCGGCCCAUCAUUGCAGAUGCUGCUGCUGUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCAGCAGCUCUGCAAAUUCGAGAGAAAAAACCCCAGUGGGUUAACCAAUCGCCGCCGCUACU
.((((......(((((((.(((((((..((((..(((((....)))))..)))).....)))))))))))))).(((....)))..(((((....)))))........))))........ ( -41.30)
>DroSec_CAF1 47847 116 - 1
UCGGCCCAUCAUUGCAGAUGCUGCUGG-GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCAGCAGCUCUGCAAAUUCGAGAGAAAAAACCCCAGUGGGUUAACCAAUCGC---CGCCGCU
.((((......(((((((.((((((((-(((..((((((....))))))......)))))))))))))))))).(((....)))..(((((....)))))........))---))..... ( -43.70)
>DroSim_CAF1 52434 119 - 1
UCGGCCCAUCAUUGCAGAUGCUGCUGG-GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCAGCAGCUCUGCAAAUUCGAGAGAAAAAACCCCAGUGGGUUAACCAAUCGCCACCGCCGCU
.((((......(((((((.((((((((-(((..((((((....))))))......)))))))))))))))))).(((....)))..(((((....)))))..............)))).. ( -43.70)
>DroEre_CAF1 39260 105 - 1
UUGGCCCAUCAUUGCAGAUGCUGCUGG-GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCA---GCUCUGCAAAUUCGAGAGAAAAAACCCCAGUGGGUUAACCAAUCG-----------
(((((((((..(((((((.((((.(((-((((..(((((....)))))..)))))))..))---))))))))).(((....))).........))))))))).......----------- ( -37.70)
>DroYak_CAF1 51654 116 - 1
UCGGCACAUCAUUGCAGAUGCUGCUGG-GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCA---GCUCUGCAAAUUCGAGAGAAAAAACCCCAGUGGGUUAACCAAUCGACGCUGCCGCG
.((((((.((.(((((((.((((.(((-((((..(((((....)))))..)))))))..))---))))))))).(((....)))..(((((....)))))........)).).))))).. ( -41.20)
>consensus
UCGGCCCAUCAUUGCAGAUGCUGCUGG_GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCAGCAGCUCUGCAAAUUCGAGAGAAAAAACCCCAGUGGGUUAACCAAUCGCC_CCGCCGCU
..(((((((..(((((((.((((((((.((((..(((((....)))))..))))....))))))))))))))).(((....))).........))))))).................... (-33.84 = -35.44 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 3,820,114 – 3,820,227
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.30
Mean single sequence MFE -33.54
Consensus MFE -27.07
Energy contribution -28.31
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -3.11
Structure conservation index 0.81
SVM decision value 2.93
SVM RNA-class probability 0.997771
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3820114 113 - 27905053
GACUCAUUUGUCCCGUCCACCUUACUUAU-------GCUUUCGGCCCAUCAUUGCAGAUGCUGCUGCUGUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCAGCAGCUCUGCAAAUUCGAG
..(((...((..(((..............-------.....)))..))...(((((((.(((((((..((((..(((((....)))))..)))).....))))))))))))))....))) ( -32.51)
>DroSec_CAF1 47884 112 - 1
GACUCAUUUGUGCCGUCCACCUUACUUAU-------GCUUUCGGCCCAUCAUUGCAGAUGCUGCUGG-GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCAGCAGCUCUGCAAAUUCGAG
..(((...((.((((..............-------.....)))).))...(((((((.((((((((-(((..((((((....))))))......))))))))))))))))))....))) ( -37.81)
>DroSim_CAF1 52474 112 - 1
GACUCAUUUGUGCCGUCCACCUUACUUAU-------GCUUUCGGCCCAUCAUUGCAGAUGCUGCUGG-GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCAGCAGCUCUGCAAAUUCGAG
..(((...((.((((..............-------.....)))).))...(((((((.((((((((-(((..((((((....))))))......))))))))))))))))))....))) ( -37.81)
>DroEre_CAF1 39289 109 - 1
GGCUCGUUUGUCCCGUUCACCUUACUUAU-------GCUUUUGGCCCAUCAUUGCAGAUGCUGCUGG-GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCA---GCUCUGCAAAUUCGAG
..((((..((..(((..............-------.....)))..))...(((((((.((((.(((-((((..(((((....)))))..)))))))..))---)))))))))...)))) ( -29.11)
>DroYak_CAF1 51694 116 - 1
GACUCAUUUGUCCCGUCCUCUUUACUUACCUAUCCACCAUUCGGCACAUCAUUGCAGAUGCUGCUGG-GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCA---GCUCUGCAAAUUCGAG
..(((...(((.(((..........................))).)))...(((((((.((((.(((-((((..(((((....)))))..)))))))..))---)))))))))....))) ( -30.47)
>consensus
GACUCAUUUGUCCCGUCCACCUUACUUAU_______GCUUUCGGCCCAUCAUUGCAGAUGCUGCUGG_GUGUAGAAAUCCAGUGAUUUUCAUAUUCAUUCAGCAGCUCUGCAAAUUCGAG
..(((...((..(((..........................)))..))...(((((((.((((((((.((((..(((((....)))))..))))....)))))))))))))))....))) (-27.07 = -28.31 +   1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:59 2006